Here we present quantitative proteomics data used in the evaluation of quantitative accuracy. A human cell line, MCF7 was split into 9 aliquotes that were spiked with a dilution series of 57 protein standards of known amounts spanning 5 orders of magnitude. The protein extracts were trypsinized, and the peptides were analysed by LC-MS using either a label-free or a label-based (TMT 6-plex and iTRAQ 8-plex) quantification approach. The iTRAQ- and TMT-labelled samples were co-analysed and separated by HiRIEF (high resolution isoelectric focusing) prior LC-MS. Raw MS data was identified and quantified under the software platform Proteome Discoverer 1.3.0.339 (Thermo Fisher Scientific Inc.) or MaxQuant software (version 1.2.0.18) (label-free data). For both protein identification and quantification at least 1 unique (i.e. a peptide that occurs in not more than one database entry) peptide was required. The false discovery rate (FDR) for peptide identification was set to 5% in all analyses. For the iTRAQ and TMT labeled samples, all MS/MS spectra were searched by SEQUEST combined with the Percolator algorithm (version 2.0) for PSM search optimization. Searches were performed against a custom made database consisting of SwissProt human sequences(uniprot.org 2012-01-17, 20242 entries), and the spiked in protein standards (57 protein sequences). Peptide FDR was calculated by a target – decoy approach.